id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9833 Graphics crash, macOS 13.5.2, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.5.2-x86_64-i386-64bit ChimeraX Version: 1.7.dev202307220101 (2023-07-22 01:01:24 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff852552700 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2730 in draw_elements File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1741 in draw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 841 in _draw_geometry File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 776 in draw_self File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 769 in draw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1556 in _draw_multiple File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1543 in draw_opaque File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 247 in _draw_scene File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 177 in draw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 206 in activate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 89 in draw_new_frame File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1044 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2880K 8 \nCG image 128K 8 \nColorSync 268K 30 \nCoreAnimation 260K 12 \nCoreGraphics 16K 3 \nCoreServices 624K 2 \nCoreUI image data 3080K 22 \nFoundation 40K 2 \nIOAccelerator 156.7M 209 \nIOKit 15.8M 19 \nIOSurface 114.3M 49 \nKernel Alloc Once 1384K 5 \nMALLOC 1.9G 172 \nMALLOC guard page 48K 11 \nMALLOC_MEDIUM (reserved) 624.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 88K 22 \nStack 146.7M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 228.6M 126 \n__CTF 824 1 \n__DATA 48.5M 773 \n__DATA_CONST 50.0M 465 \n__DATA_DIRTY 1850K 235 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.3M 146 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 969.1M 779 \ndyld private memory 292K 4 \nmapped file 223.2M 57 \nshared memory 59.3M 144 \n=========== ======= ======= \nTOTAL 5.0G 3353 \nTOTAL, minus reserved VM space 4.2G 3353 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f8f8d273ee71c202296cc08b849c35bf80acc5fe"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""64d14f3e1008ca2fac17a163"" }, ""deploymentId"" : 240000064 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""3a3cf641-8471-4e4e-9ad4-81d0ede970fd"", ""experimentId"" : ""64a84dae90d82611a0bd7d3d"", ""deploymentId"" : 400000004 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/mi/Documents/000-download papers/5btc.pdb"" 5btc.pdb title: Crystal structure of A topoisomerase II complex [more info...] Chain information for 5btc.pdb #1 --- Chain | Description | UniProt A C | DNA gyrase subunit A | GYRA_MYCTU 2-500 B D | DNA gyrase subunit B | GYRB_MYCTU 426-675 E H | DNA substrate 24-mer ggtcatgaatgactatgcacgtaa | F G | DNA substrate 24-mer ttacgtgcatagtcattcatgacc | Non-standard residues in 5btc.pdb #1 --- CPF — 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic acid (ciprofloxacin) MG — magnesium ion > hide #1.1 models > hide #1.2 models > open 5btc fromDatabase rcsb_bio maxAssemblies 1 Summary of feedback from opening 5btc fetched from rcsb_bio --- notes | Fetching compressed 5btc bioassembly 1 from https://files.rcsb.org/download/5btc-assembly1.cif Fetching CCD CPF from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CPF/CPF.cif 5btc bioassembly 1 title: Crystal structure of a topoisomerase II complex [more info...] Chain information for 5btc bioassembly 1 #2 --- Chain | Description A C | DNA gyrase subunit A B D | DNA gyrase subunit B E H | DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA F G | DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC Non-standard residues in 5btc bioassembly 1 #2 --- CPF — 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic acid (ciprofloxacin) MG — magnesium ion Opened 1 biological assemblies for 5btc > hide #!1 models > hide :gol > hide solvent > hide protein > select clear > hide DNA Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > coulombic protein The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 5btc bioassembly 1 #2/B VAL 675 OXT 5btc bioassembly 1 #2/D VAL 675 OXT 5btc.pdb #1/D VAL 675 OXT 5btc.pdb #1/B VAL 675 OXT Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.in.mol2 -fi mol2 -o /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.in.mol2); atoms read (36), bonds read (36).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Assigning partial charges to residue PTR (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.in.mol2 -fi mol2 -o /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.in.mol2); atoms read (37), bonds read (37).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.in.mol2 -fi mol2 -o /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.in.mol2); atoms read (37), bonds read (37).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.in.mol2 -fi mol2 -o /var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.in.mol2); atoms read (36), bonds read (36).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Coulombic values for 5btc.pdb_A SES surface #1.3: minimum, -20.85, mean -1.74, maximum 14.01 Coulombic values for 5btc.pdb_B SES surface #1.4: minimum, -20.08, mean 0.02, maximum 14.55 Coulombic values for 5btc.pdb_C SES surface #1.5: minimum, -22.98, mean -1.77, maximum 13.69 Coulombic values for 5btc.pdb_D SES surface #1.6: minimum, -20.10, mean 0.10, maximum 19.59 Coulombic values for 5btc bioassembly 1_A SES surface #2.2: minimum, -20.85, mean -1.74, maximum 14.01 Coulombic values for 5btc bioassembly 1_B SES surface #2.3: minimum, -20.08, mean 0.02, maximum 14.55 Coulombic values for 5btc bioassembly 1_C SES surface #2.4: minimum, -22.98, mean -1.77, maximum 13.69 Coulombic values for 5btc bioassembly 1_D SES surface #2.5: minimum, -20.10, mean 0.10, maximum 19.59 > color nucleic tan > cartoon style nucleic xsection round width 1.5 thickness 1.5 > nucleotides stubs > nucleotides #!2 atoms > style nucleic & #!2 stick Changed 2469 atom styles > nucleotides #!2 atoms > style nucleic & #!2 stick Changed 2469 atom styles > style #!2 stick Changed 25950 atom styles > nucleotides #!2 fill > style nucleic & #!2 stick Changed 2469 atom styles > lighting simple > lighting shadows true > lighting shadows false > lighting flat > ui tool show ""Side View"" > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > view orient > nucleotides stubs ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Registration OpenGL version: 4.1 INTEL-20.6.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.5.1, Qt 6.5.1 Qt runtime version: 6.5.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.5.2 (22G91) Kernel Version: Darwin 22.6.0 Time since boot: 11 minutes, 4 seconds Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal S24E360: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46.1 ChimeraX-AtomicLibrary: 10.0.8 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.4 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202307220101 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.2 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.31.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.41.1 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.7 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.9.1 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.5.1 PyQt6-Qt6: 6.5.1 PyQt6-sip: 13.5.1 PyQt6-WebEngine-commercial: 6.5.0 PyQt6-WebEngine-Qt6: 6.5.1 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal Graphics nonchimerax all ChimeraX